Make preview png work correctly

- missed a lib function in the preview pipeline
- converted it to a result container
- integrate it into the pipeline

Author: snregales

packages/scratch-core/src/conversion/display.py

@@ -1,10 +1,11 @@
-from .exceptions import NegativeStdScalerException
 import numpy as np
 from parsers.data_types import ScanImage
 from utils.array_definitions import ScanMap2DArray
+from returns.result import safe
+from utils.logger import log_railway_function
 
 
-def normalize(
+def _normalize(
     input_array: ScanMap2DArray, lower: float, upper: float
 ) -> ScanMap2DArray:
     """Perform min-max normalization on the input array and scale to the [0, 255] interval."""
@@ -15,7 +16,7 @@ def normalize(
     return (input_array - lower) / (upper - lower) * 255.0
 
 
-def clip_data(
+def _clip_data(
     data: ScanMap2DArray, std_scaler: float
 ) -> tuple[ScanMap2DArray, float, float]:
     """
@@ -28,16 +29,19 @@ def clip_data(
     :returns: A tuple containing the clipped data, the lower bound, and the upper bound of the clipped data.
     """
     if std_scaler <= 0.0:
-        raise NegativeStdScalerException("`std_scaler` must be a positive number.")
+        raise ValueError("`std_scaler` must be a positive number.")
     mean = np.nanmean(data)
     std = np.nanstd(data, ddof=1) * std_scaler
     upper = float(mean + std)
     lower = float(mean - std)
-    clipped = np.clip(data, lower, upper)
-    return clipped, lower, upper
+    return np.clip(data, lower, upper), lower, upper
 
 
-def get_array_for_display(image: ScanImage, std_scaler: float = 2.0) -> ScanMap2DArray:
+@log_railway_function("Failed to retreive array for display")
+@safe
+def get_array_for_display(
+    scan_image: ScanImage, *, std_scaler: float = 2.0
+) -> ScanImage:
     """
     Clip and normalize image data for displaying purposes.
 
@@ -48,6 +52,8 @@ def get_array_for_display(image: ScanImage, std_scaler: float = 2.0) -> ScanMap2
     :param std_scaler: The multiplier `S` for the standard deviation used above when clipping the image.
     :returns: An array containing the clipped and normalized image data.
     """
-    clipped, lower, upper = clip_data(data=image.data, std_scaler=std_scaler)
-    normalized = normalize(clipped, lower, upper)
-    return normalized
+    return ScanImage(
+        data=_normalize(*_clip_data(data=scan_image.data, std_scaler=std_scaler)),
+        scale_x=scan_image.scale_x,
+        scale_y=scan_image.scale_y,
+    )

packages/scratch-core/tests/conversion/test_display.py

@@ -13,5 +13,5 @@ def test_get_image_for_display_matches_baseline_image(
     scan_image_with_nans: ScanImage,
 ):
     verified = np.load(BASELINE_IMAGES_DIR / "display_array.npy")
-    display_image = get_array_for_display(scan_image_with_nans)
-    assert_array_almost_equal(display_image, verified)
+    display_image = get_array_for_display(scan_image_with_nans).unwrap()
+    assert_array_almost_equal(display_image.data, verified)

src/preprocessors/pipelines.py

@@ -2,6 +2,7 @@
 from http import HTTPStatus
 from pathlib import Path
 
+from conversion.display import get_array_for_display
 from conversion.subsample import subsample_array
 from fastapi.exceptions import HTTPException
 from image_generation.data_formats import ScanImage
@@ -101,7 +102,8 @@ def surface_map_pipeline(parsed_scan: ScanImage, output_path: Path, parameters:
 def _preview_pipeline(parsed_scan: ScanImage, output_path: Path) -> IOResultE[Path]:
     return flow(
         parsed_scan,
-        scan_to_image,
+        get_array_for_display,
+        bind(scan_to_image),
         bind(partial(save_image, output_path=output_path)),
     )